combp {ENmix} | R Documentation

## Identification of differentially methylated regions

### Description

To identify differentially methylated regions using a modified comb-p method

### Usage

           combp(data,dist.cutoff=1000,bin.size=310,seed=0.01,
                 region_plot=TRUE,mht_plot=TRUE,nCores=10,verbose=TRUE)

### Arguments

`data` | A data frame with colname name "chr","start", "end","p" and "probe", indicating chromosome (1,2,3,...,X,Y), chromosome start and end position, P value and probe names
`dist.cutoff` | Maximum distance in base pair to combine adjacent DMRs
`bin.size` | bin size for autocorrelation calculation
`seed` | FDR significance threshold for initial selection of DMR region
`region_plot` | If TRUE, regional plots will be generated
`mht_plot` | If TRUE, mahattan plot will be generated
`nCores` | Number of computer cores will be used in calculation
`verbose` | If TRUE, detailed running information will be printed

### Details

The input should be a data frame with column names "chr","start", "end","p", and "probe", indicating chromosome number, start position, end position, P value and probe name. The function use a modified comb-p method to identify differentially methylated regions. DMR results will be stored in a file with name resu_combp.csv. If plot options were selected, two figure files will be generated: mht.jpg and region_plot.pdf.

### Author(s)

Liang Niu, Zongli Xu

### References

Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinfomatics 2012

Zongli Xu, Changchun Xie, Jack A. Taylor, Liang Niu, ipDMR: Identification of differentially methyl-ated regions with interval p-values, Bioinformatics 2020

### Examples

    dat=simubed()
    names(dat)
    #seed=0.1 is only for demonstration purpose, it should be smaller than 0.05 or 0.01 in actual study.
    combp(data=dat,seed=0.1)

[Package ENmix version 1.30.03 Index]